How to smooth a mesh imported in .wrl format?
I'm fairly new to Blender myself, so take what I say with a grain of salt, but in general, there's two ways to deal with this, depending on what you need the file for.

The easiest way is to just go object mode > select the object (for all objects, just press "A") > right click > shade smooth. That only makes it look more smooth though, it doesn't actually change anything about the file.

To actually change your mesh, use the subdivision surface modifier. In this video, both approaches are explained fairly well:

https://youtu.be/RaT-uG5wgUw?list=PLjEaoINr3zgEq0u2MzVgAaHEBt--xLB6U&amp;t=584

PyMol itself is most likely using some type of modifier/effect when displaying Objects, while the base object has a rather low vertex count.